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Course
Description
This course is designed to help your transition into graduate
school and in particular to bioengineering which is in the act
of defining itself. Bioengineering is pre-eminently an integrating
discipline, at the intersections of virtually all disciplines
in biology and engineering. This course and bioengineering itself
are not engineering tools applied to topics in physiology, anatomy,
biochemistry, etc. Neither are they watered down biology to jump-start
engineers. The biological disciplines benefit from the analyses,
quantification and simulations of engineering disciplines. Similarly
engineering benefits from learning about the complexity, redundancy
and degeneracy in functioning cells, organs and systems.
The major content, elements and principles to be taught are:
- protein-protein
interactions; aspects of recognition and as machines coupling
a thermodynamic driving force with a mechanical, osmotic and
electrical work.
- function at scales
differing by 9 orders of magnitude, from nanometers to meters
- metabolic machines
are computing and signaling machines; metabolic processes are
chemical networks driving exergonic biological functions; these
chemical reactions occur in what is essentially a liquid medium
(important discussion of this matter in lectures 16 and 17)
- membrane separate
functional domains, and channels are inter-domain communication
machines
- neural control
of components and systems, and regulation of function
This course uses muscle in as the physiological material to develop
these themes. Muscle is one of the best developed topics among
biological systems, yet one that continues to provide challenging
problems and requires significant technical and experimental development
for current research. Students may learn more about the function
of muscle than they might think they need in the process; but
that process is the key not the information about muscle per se.
We will show that with this topic we can span an enormous range
of biological and engineering concepts, and assist you to develop
a discerning attitude to scientific advancement of knowledge.
Students will also develop the intellectual tools to enable them
to learn new material by their own reading and analysis, and especially
by developing clever hypotheses, working out their quantitative
aspects and relationships as predictions, working out definitive
experimental tests and designing the tools sufficient to conduct
those tests.
In this course muscle is the examplar and surrogate for all of
physiology. But many other topics can be similarly treated, and
will be in other courses, e.g. cardiovascular and respiratory
systems as liquid and gas transport respectively; neural and endocrine
systems is signaling, control and integration; biomaterials as
interfaces, cell surface mimmetics; kidney as waste treatment
and reclamation machines.
Framing
the questions for a new course at the interface of bioengineering
<-> physiology Principles of engineering shed new light on
issues in biology; concepts from biology challenge engineering
to evolve new tools for study and analysis. A major conceptual
limitation for biologists is a weak ability to construct paradigms
to account for the extremely well organized complexity of living
systems. Current facts, information, concepts, approaches and
even the logic of systems of differential equations for experimental
design, simulation and analysis are often not sufficient for this
task. We are continually seeking more and more data. But in order
to make progress in this area, we must wrench ourselves from this
feeding frenzy of data for data's sake. Instead we need to find
basic, even simple, relationships among the components we study.
Structure and function are intimately related over an enormous
range of sizes -- from nanometers to meters. We need integrated
systematic analyses and concepts. Historically there were first
concepts for dealing with organized simplicity, typified by the
Newtonian revolution of the 18th century in "classical" mechanics.
Later concepts were developed for understanding disorganized complexity
with the development of the ideal gas law and then of statistical
and quantum mechanics. Now we are in the midst of dealing with
organized complexity -- the unique feature of living systems which
follow algorithms evolved by Nature. Genetic codes are available
but the functional algorithms remain opaque to our visualization.
We do not yet have concepts to investigate or understand the organized
complexity so evident in living beings that grow, adapt, reproduce
and evolve. Some say "the whole is greater than the sum of its
parts". If so, how so? Frankly, the goal of this course is outrageously
ambitious: to propose the relevant and significant questions and
help you to develop the factual knowledge, critical analysis skills,
and professional attitude necessary to become innovative and productive
bioengineers in analysis and integration. 'Systems' thinking has
benefited insufficiently from the rich information of cellular
and molecular mechanisms. Likewise those working at that level
of highly reduced mechanism do not commonly develop tools for
building living systems into a coherent whole. At our University,
as at most others, 'cellular' and 'molecular' investigators are
largely polarized from 'systems' and 'integrative' investigators.
The goal in this course is to take steps to unite both sets of
views. The primary benefit of this course will be the great intellectual
challenge of a journey to create a synthetic strategy and approach
that does not deny molecular biology its integrative potential,
nor rob systemic thinking of its mechanistic significance.
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Grading
Policy
Educational Contract: We need to match your goals and
our expectations. Our goal is to make a supportive environment
for your learning in which you can communicate freely with any
faculty or teaching assistant. Part of the information we want
to collect during the first lecture is your background, concurrent
courses and your expectations and goals for this course. Our challenge
is to match our expectations with yours over the next 11 weeks.
We will discuss this 'educational contract' between students and
faculty in the first lecture, and thereafter as often as useful.
Evaluation and Feedback to students: Our goal is to have
you mature as independent scientists and engineers. Regular and
continuous communication is very important in these matters. We
will give each student our evaluation of his or her work on each
problem set and laboratory report; these will be in the form of
written comments on each report.. These reports are intended to
be your own independent work and we will evaluate your work in
this light. The primary purpose of these evaluations (nominally
as grades) is to assist you in evaluating your own progress and
for you to receive our evaluation of your progress and suggestions
for improvement. The proportion of your final grade in the course
will be determined as follows:
Problem sets 35%
Laboratory reports 25%
Mid term exam 20%
Final exam 20%
Evaluation and Feedback to faculty and TA's We would very
much appreciate feedback from you on all aspects of the course,
especially if your expectations are not being met. The diversity
of the students and their backgrounds are great, so what may be
known and familiar to some will be new and initially puzzling
to others. You will learn that the diversity in the faculty is
also great. Keep in mind that this is the first time this sort
of course has been offered by the Bioengineering Department; consequently,
its design and organization are still developing. We expect some
things to work better than others. As you identify and share with
us those aspects that work and those that do not, we will be able
to add to what works and fix what doesn't.
Partnering: This is a graduate level course and you are
seeking development of your skills, attitudes and knowledge base;
you are not working for high grades per se anymore. At the same
time we encourage you to collaborate on appropriate aspects of
the course work and collaboration will be required in the experimental
labs. If it suits you we recommend you aggregate into small study
groups. It is part of professional training to be able to carry
on and distinguish both independent and collaborative work. In
that sense shared ideas and information need to be noted, recognized
and respected. Copying and other forms of plagiarism are of course
major violations of professional and scientific ethics. In this
sense our evaluation of your work will have meaning to you only
to the extent that you know and report your own work.
We encourage you to form study groups of about 4; these can be
laboratory groups and/or simulation groups. Even though you do
this, each student is responsible for her or his written material
independently. You are not developing properly if you commonly
generate answers, approaches, ideas, etc. only from the work of
your partners. Only with your individual effort will you develop
rapidly and sufficiently as a critical, knowledgeable, imaginative
bioengineer.
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Required
Readings
Textbooks
1. Alberts et al., Molecular
Biology of the Cell
Supplimental
(Required) Reading
listed for each lecture
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Other Items
Notes will be posted following
each lecture.
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